Re: [pybliographer-1.2.6.2] bug in isifile.py

On Fri, May 20, 2005 at 08:04:10AM +0000, Peter Schulte-Stracke wrote:
> Am 19.05.2005 09:15:46 schrieb(en) Pavol Juhas:
> 
> >I was trying to use pybliographer 1.2.6.2 with larger
> >ISI files, but it did not work as it was crashing during
> >bibopen  with "index out of range" error.  I was able to track  
> >the problem to isifile.py, and the attached patch should fix  
> >it.  Let me know if there has already been some other solution  
> >in development versions.
> 
> From the patch it appears that there was a problem with the
> code that corrects the capitalisation of journal titles (they  
> come in several variants, none of which is correct, but can be  
> combined to yield a correct one). Thus it would not be a  
> question of the size of the input file per se.
> 
> The code is intended to match the correctly capitalised title  
> abbreviation with  the full but uppercase title.
> 
> I'm afraid I don't see at the moment what went wrong with the  
> code -- do you have a sample of title fields for me?

As far as I understand, the original code obtains capitalized 
journal title from the "SO" and "JI" fields in ISI entry.
When doing that, it assumes "JI" field contains at least as many 
words as the "SO" field.  However there are ISI entries, where this 
is not true, and the original code would crash on reading them.  See 
the attached file for an example.

Cheers,

Pavol

PT J
AU Zavodszky, MI
   Ming, L
   Thorpe, MF
   Day, AR
   Kuhn, LA
TI Modeling correlated main-chain motions in proteins for flexible
   molecular recognition
SO PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
DT Article
C1 Michigan State Univ, Dept Biochem & Mol Biol, Prot Struct Anal & Design Lab, E Lansing, MI 48824 USA.
   Michigan State Univ, Dept Phys & Astron, E Lansing, MI 48824 USA.
   Arizona State Univ, Dept Phys & Astron, Tempe, AZ 85287 USA.
   Michigan State Univ, Ctr Biol Modeling, E Lansing, MI 48824 USA.
RP Kuhn, LA, Michigan State Univ, Dept Biochem & Mol Biol, Prot Struct
   Anal & Design Lab, E Lansing, MI 48824 USA.
EM kuhnl-mhe/[email protected]
TC 0
J9 PROTEINS
JI Proteins
PD NOV 1
PY 2004
VL 57
IS 2
BP 243
EP 261
UT ISI:000223926200002
ER